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Re: [MUMmer-help] nucmer misses alignments with less input sequences
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From: Adam P. <aph...@gm...> - 2014-10-15 20:05:54
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Michael, Thank you for the detailed report. I will be sure to take a look at this. -Adam On Mon, Oct 13, 2014 at 12:03 PM, Michael Hiller <hi...@mp...> wrote: > Hi, > > I am using nucmer to align DNA sequences and during some playing around > with my input data, I noticed the following bug or strange behavior: > > > I aligned two small files (input.fa with sequence "a" and "b" against > input2.fa with sequence "c") and found a hit between "a" and "c" > > cat input.fa > >a > > GTGTCTTTGGTGCACTGGATGTAGATGGATTCTTGCGCCCATTCACGATTGTGGTAGAAGGGCTAGTAAAGGTGGAGTGGATAATCCAACCCGCAACTCCGATATGAATGGCCGTCTTTTGATCAGCCGCATATTAGACTTAACGTGCTCAAAAACACGGTTCATAATCCTTGATTATGCTGTTGACCAGCTTGCTGGCCAGTGTAGGATCAATTCGTTTATTATATAAGTCCTGCAGTCAAAGATCAGTAAGAAATTATTGATTGCTTTCTAACGTTTTTTCCCTTTCATGAAGTGCTTGGGGTTTTGCCAAAGAAATCCTTTAGCCTTTAGTAGTAAATAAGCAGACTAGAGTCCACATACATCGACAATATATCAGCTTCTGCTGGCGGCGAATCAGAGGGGCCGCTGTCGCCTCCACCTATGAGGCCCCTCAGGGCGAGCTGGCTCCATTGGGAGTAGATGGAACACTGGCGGCTTCAGTGGGTTAGACCTGTGTAATAGAGACACGCCAGATTTGCACCCTGCCCCTGGTGGTGCACTGTCGCCAATCGCCCAAGCGTGGCGACACCTTGATCCTGGCCTGTTCCCGATTGGGCAATCGGGCCTGGGGGGCAGTCGTTCCAGGCCCAAATTAGCTGCATTGCATCGTGTGGCATCACTGGCGCACCTGCAGTGGCGCCTCCGGCCCTCGCCTTCCTGCTCCTACTGTGTCAGCCAGTGCATTCACGCATCTATCCATAGAGATACATTTGGGTGTGCCTGGGCTTTCGCACCAGCGATTAACTTTTTGCTGCCAGTTTCCTCCTTGGCTTACTGCAGGCGGCAAGATGGAACAGCAGAATGTCAGCTGACATTCGTTCACAAAAGATCATGAAACTAACACCAGGGCCGGAATTGTAGAGATGTATCCACTTCCTTGTGTGTTTAGGAACTAACACAAGTTGGTGGATGGGTGGTAGTAACAATGACAGAAGAATTGCCACCCGG > >b > > AAAAGAGAGCATTTATGCTTTTGAATTTAACTTAAGTTTGATGCACTAAAATAATAAAGGTATTCGATGTACTGTTCTATTTAAGTGCATAAAACTATTTTTTGTAAGGGTGCTATATCCTTTTTTCAGATAGATTCTTTGTTGATTCTCTTCCTTTTGATAAGAAGGAGTAGTTCCTGGTCAAGAGGCTAAAGTGTGGAAATGACCACATTTTCCACACTTTCTGCCAACCAGTGACAACATATCATAGGTGGCTAGCAGTGCAGAAAGAAGTCAAAAAGGTGTCCTGGCTTCAGGTTAGCCTCCTCCAGCCTAGCCAACAAAATGTGACTGCTTTGAATTCTCTGTAAACAAGAGAATTCATAAAAGCCATAAAACCAAAAAAAAAAACTCTGCACACTTCCAAGCAGGAGCTGTAGCTGGCAGATGTAGATCTAAGTTGGGTTTTATCCAGCTAGGGCCAATTATCCTCTCCTGTTCTGTTAGCCAAATTGTGGGATTCTCTAAAAGCCCAGAAATTACTCGCTGATAGAGTTGGAAACACCTAGACAAAGGGCTAAAAAGTTCAGGAGCATTAAAAAATGGTATTCCTGCATTGAACAGTACTCGCCCTCCAAAGAATTCATCTATTTGAAGGTTAAAAATGTGGGATCAAATATAAAAGTAGATCCTTAACCCAATACCAATGTGTGTTTACGCAACATTAAGGCTTTTATTTACAAGATTTGGGAGAAGAGAAGATGGATGAAGGCTGTTGAGTAAAATAATGAAACAGATGAATTTTTCCCCTTGAAAACAGAGACACAGGTTAAACCAGGAGGGGTTGGAGAATAGCCAATGGTTAACATGTATGCCCAACTGATGAGATGTTTTTAAAGATGATAAAGAGAAGGAGGGTTCCTTCCTGGTTGAGTAGAAACGGAGGGTGGCTTTTTTGAAGAGGAGCGAAA > cat input2.fa > >c > > TATAAATAGCTAAATACATAACTAATGTTATGAATTCTTCTAGAAAATGTCAAGAAGTCATTGCAATTTATTTCTCGCTTGCAACTTTGAAACAATATTGTATGCTTTAGGTTCCACTTTCCACTTTTTTCTTGCCTCTGTCTGGTTGATTATTTTTGTGTCAGTGGTGCCACCTCGTGGAGTTTAAGTTTTACTGGCAAACTCTCCTTTTAAAATAAACACAGTGTAGTATTATTATATGGGAAAGAGAACAGGATTCTTGTGCATTCAGTAGTTATACAGAACACCTGCTTAAATTTTGTCTTTGGTACAACTATTAGAAGCACAGAAGTCCTTCTAACTGTACTAAAGTGGATCATTGCAAAGTCATTATGAAAAGAATTCTAACAAAACGCATACATTGCAACAGAATGAAAACATGGCAATTCTTGTATTTTATAACCCATCCAAAACTTGTGTTAGTTCCTAAACACAAGGAATGGAGTACATCTACAGTTCTGTTAGTTCATGATTTTTGTGAACATGTCAGTGACATTCTGCTGTTCCATCTTGCCGCCTGCAGTAGCCAAGAGAAGTGGCAGCAAAAAGTTAATCACTGGTGCAAACCCAGCAACCAAATTATCTCTATGGATAATGGTGAAGGCACTGGCTGACACAGTAGGAGATGAAGGCGAGGCGAGGCGAGGCCATGCAGTGCGCAGTGATGCACAGATGCAATCAGCTAATTGGGCCTGAACGATGCCCCAGGCCCGATTGCCCAATCGAACAGGCAGGATCAATGTGTCGCAGTGGCCGGGACA > nucmer --maxmatch -l 11 -b 1000 -g 1000 input.fa input2.fa ; show-coords > out.delta > > gives: > NUCMER > > [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% > IDY] | [TAGS] > > ===================================================================================== > 565 985 | 787 420 | 421 368 | 83.89 | > a c > > > > Now, if I remove sequence "b" from input.fa that shows no alignment, the > alignment between "a" and "c" is not found anymore > > cat input.fa > >a > > GTGTCTTTGGTGCACTGGATGTAGATGGATTCTTGCGCCCATTCACGATTGTGGTAGAAGGGCTAGTAAAGGTGGAGTGGATAATCCAACCCGCAACTCCGATATGAATGGCCGTCTTTTGATCAGCCGCATATTAGACTTAACGTGCTCAAAAACACGGTTCATAATCCTTGATTATGCTGTTGACCAGCTTGCTGGCCAGTGTAGGATCAATTCGTTTATTATATAAGTCCTGCAGTCAAAGATCAGTAAGAAATTATTGATTGCTTTCTAACGTTTTTTCCCTTTCATGAAGTGCTTGGGGTTTTGCCAAAGAAATCCTTTAGCCTTTAGTAGTAAATAAGCAGACTAGAGTCCACATACATCGACAATATATCAGCTTCTGCTGGCGGCGAATCAGAGGGGCCGCTGTCGCCTCCACCTATGAGGCCCCTCAGGGCGAGCTGGCTCCATTGGGAGTAGATGGAACACTGGCGGCTTCAGTGGGTTAGACCTGTGTAATAGAGACACGCCAGATTTGCACCCTGCCCCTGGTGGTGCACTGTCGCCAATCGCCCAAGCGTGGCGACACCTTGATCCTGGCCTGTTCCCGATTGGGCAATCGGGCCTGGGGGGCAGTCGTTCCAGGCCCAAATTAGCTGCATTGCATCGTGTGGCATCACTGGCGCACCTGCAGTGGCGCCTCCGGCCCTCGCCTTCCTGCTCCTACTGTGTCAGCCAGTGCATTCACGCATCTATCCATAGAGATACATTTGGGTGTGCCTGGGCTTTCGCACCAGCGATTAACTTTTTGCTGCCAGTTTCCTCCTTGGCTTACTGCAGGCGGCAAGATGGAACAGCAGAATGTCAGCTGACATTCGTTCACAAAAGATCATGAAACTAACACCAGGGCCGGAATTGTAGAGATGTATCCACTTCCTTGTGTGTTTAGGAACTAACACAAGTTGGTGGATGGGTGGTAGTAACAATGACAGAAGAATTGCCACCCGG > cat input2.fa > >c > > TATAAATAGCTAAATACATAACTAATGTTATGAATTCTTCTAGAAAATGTCAAGAAGTCATTGCAATTTATTTCTCGCTTGCAACTTTGAAACAATATTGTATGCTTTAGGTTCCACTTTCCACTTTTTTCTTGCCTCTGTCTGGTTGATTATTTTTGTGTCAGTGGTGCCACCTCGTGGAGTTTAAGTTTTACTGGCAAACTCTCCTTTTAAAATAAACACAGTGTAGTATTATTATATGGGAAAGAGAACAGGATTCTTGTGCATTCAGTAGTTATACAGAACACCTGCTTAAATTTTGTCTTTGGTACAACTATTAGAAGCACAGAAGTCCTTCTAACTGTACTAAAGTGGATCATTGCAAAGTCATTATGAAAAGAATTCTAACAAAACGCATACATTGCAACAGAATGAAAACATGGCAATTCTTGTATTTTATAACCCATCCAAAACTTGTGTTAGTTCCTAAACACAAGGAATGGAGTACATCTACAGTTCTGTTAGTTCATGATTTTTGTGAACATGTCAGTGACATTCTGCTGTTCCATCTTGCCGCCTGCAGTAGCCAAGAGAAGTGGCAGCAAAAAGTTAATCACTGGTGCAAACCCAGCAACCAAATTATCTCTATGGATAATGGTGAAGGCACTGGCTGACACAGTAGGAGATGAAGGCGAGGCGAGGCGAGGCCATGCAGTGCGCAGTGATGCACAGATGCAATCAGCTAATTGGGCCTGAACGATGCCCCAGGCCCGATTGCCCAATCGAACAGGCAGGATCAATGTGTCGCAGTGGCCGGGACA > nucmer --maxmatch -l 11 -b 1000 -g 1000 input.fa input2.fa ; show-coords > out.delta > > gives: > NUCMER > > [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% > IDY] | [TAGS] > > ===================================================================================== > > > > I called mummer and mgaps manually on the .ntref file and it seems that > while mummer outputs something, mgaps removes the alignment. > > Could you please have a look if this is a bug, and if not tell me which > mgaps parameters would keep that alignment? > > > Thanks a lot > - Michael > > > > > > > > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://p.sf.net/sfu/Zoho > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > |
